Patches item #2405759, was opened at 2008-12-08 03:09
Message generated for change (Comment added) made by rajarshi
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Category: None
Group: Needs Review
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Egon Willighagen (egonw)
Assigned to: Nobody/Anonymous (nobody)
Summary: upgrade to jni-inchi 0.5
Initial Comment:
Sam has released a new version of his bridge to the InChI libraries, and version 0.5 adds support for 64 bit systems, as well as OS/X, and on top of that InChIKey generation. Attached a patch for the cdk-1.2.x/ branch.
Please verify by two senior developers (and anyone else), as I like to see it included in the cdk-1.2.x/ branch, which is formally in freeze. The patch does not change any API methods, except for adding a getInChIKey() method (see patch). A unit test assertion for InChIKey generation is added.
The full git branch is up here:
http://github.com/egonw/cdk/commits/newJNIInChI
----------------------------------------------------------------------
>Comment By: Rajarshi Guha (rajarshi)
Date: 2009-01-20 16:16
Message:
Looks good - it's be useful to include a note in the docs regarding 64 bit
Linux (I don't have a 64 bit OS anymore to test on)
----------------------------------------------------------------------
Comment By: Egon Willighagen (egonw)
Date: 2009-01-20 14:18
Message:
OS/X works, 32 bit and 64 bit.
Linux 64bit has been reported not to work from within Bioclipse.
----------------------------------------------------------------------
Comment By: Egon Willighagen (egonw)
Date: 2008-12-10 14:19
Message:
Excellent point! We need 64bit and OS/X Nightly servers :)
Ummm... what we also need, is a Nightly meta server, which keeps track of
different instances of nightly's... and maybe put (comparable) test results
in a table... which would make it easier to compare platform dependencies,
as well as an easy way to autocompare (comparable) branches... say a patch
branch for cdk1.2.x/... not so much thinking about comparing trunk with
cdk1.2.x/ here...
----------------------------------------------------------------------
Comment By: Rajarshi Guha (rajarshi)
Date: 2008-12-10 10:31
Message:
Patch looks fine to me. Has this been tested on OS X or Linux 64 bit?
----------------------------------------------------------------------
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Patches item #2501495, was opened at 2009-01-12 16:00
Message generated for change (Comment added) made by egonw
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Category: None
Group: None
>Status: Closed
>Resolution: Works For Me
Priority: 5
Private: No
Submitted By: Stefan Kuhn (shk3)
Assigned to: Egon Willighagen (egonw)
Summary: GaussianInputWriter gives empty result
Initial Comment:
I wrote a test case for the GaussianInputWriter, which is attached (there was no test till now). There is one real problem:
It gives am empty result. I also found this in JCP. This means the class is useless. I couldn't find the problem by a quick look, but will try again. Anybody else is wellcome to join in.
Also the test of the accepts fails, but this might be because I did not understand the concept of this accepts.
----------------------------------------------------------------------
>Comment By: Egon Willighagen (egonw)
Date: 2009-01-20 22:01
Message:
Unit test works in cdk1.2.x.
----------------------------------------------------------------------
Comment By: Stefan Kuhn (shk3)
Date: 2009-01-12 17:20
Message:
Committed the class to trunk
----------------------------------------------------------------------
Comment By: Egon Willighagen (egonw)
Date: 2009-01-12 16:51
Message:
I wrote that class... I know what the expected output should be. Please do
add the unit test, @cdk.bug annotation, etc, and I'll look at it asap.
----------------------------------------------------------------------
Comment By: Rajarshi Guha (rajarshi)
Date: 2009-01-12 16:30
Message:
In that case I'd put in an Assert.fail() so that we know the test requires
some more work - unless somebody can provide an example of a Gaussian input
for the molecule in question
----------------------------------------------------------------------
Comment By: Stefan Kuhn (shk3)
Date: 2009-01-12 16:18
Message:
Since I have no idea what the output is supposed to look like, I can't
really add a test for it...
----------------------------------------------------------------------
Comment By: Rajarshi Guha (rajarshi)
Date: 2009-01-12 16:14
Message:
I took a quick look at the patch. Two suggestions
* Remove the println
* Also include an assertion that checks that the output is correct (by
checking for the presence/position of certain substrings)
----------------------------------------------------------------------
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Patches item #2405759, was opened at 2008-12-08 09:09
Message generated for change (Comment added) made by egonw
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Category: None
Group: Needs Review
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Egon Willighagen (egonw)
Assigned to: Nobody/Anonymous (nobody)
Summary: upgrade to jni-inchi 0.5
Initial Comment:
Sam has released a new version of his bridge to the InChI libraries, and version 0.5 adds support for 64 bit systems, as well as OS/X, and on top of that InChIKey generation. Attached a patch for the cdk-1.2.x/ branch.
Please verify by two senior developers (and anyone else), as I like to see it included in the cdk-1.2.x/ branch, which is formally in freeze. The patch does not change any API methods, except for adding a getInChIKey() method (see patch). A unit test assertion for InChIKey generation is added.
The full git branch is up here:
http://github.com/egonw/cdk/commits/newJNIInChI
----------------------------------------------------------------------
>Comment By: Egon Willighagen (egonw)
Date: 2009-01-20 20:18
Message:
OS/X works, 32 bit and 64 bit.
Linux 64bit has been reported not to work from within Bioclipse.
----------------------------------------------------------------------
Comment By: Egon Willighagen (egonw)
Date: 2008-12-10 20:19
Message:
Excellent point! We need 64bit and OS/X Nightly servers :)
Ummm... what we also need, is a Nightly meta server, which keeps track of
different instances of nightly's... and maybe put (comparable) test results
in a table... which would make it easier to compare platform dependencies,
as well as an easy way to autocompare (comparable) branches... say a patch
branch for cdk1.2.x/... not so much thinking about comparing trunk with
cdk1.2.x/ here...
----------------------------------------------------------------------
Comment By: Rajarshi Guha (rajarshi)
Date: 2008-12-10 16:31
Message:
Patch looks fine to me. Has this been tested on OS X or Linux 64 bit?
----------------------------------------------------------------------
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https://sourceforge.net/tracker/?func=detail&atid=320024&aid=2405759&group_id=20024

Hi,
The application stuff from the cdk was removed, so things like
MoleculeViewer2D are no longer in there.
We haven't worked out yet where the GUI builder parts like
MoleculeTables, ChemTreeView and so on will live, but they will I
suppose (I assume) be based on the new rendering architecture. See
Rajarshi's recent battle with this on the jchempaint list for
instructive details :)
I would very much like there to be some place that developers who want
a 2D molecule viewer or editor as part of their project can download a
single package with, or without the whole of the rest of the cdk.
gilleain
On Wed, Jan 14, 2009 at 10:22 AM, tim0815 <ottmar@...> wrote:
>
> Hi I downloaded and included cdk 1.1.4.jar in my Project and can not use
> MoleculeViewer2D.display why is the MoleculeViewer2D not included in the jar
> file? do I have to add an older library like cdk1.0.4.jar additional to the
> 1.1.4?

Dear Sebastian,
I am not aware of any descriptors for molecular cross-section. Off the
top of my head, it seems as if that would require prediction of the 3D
coordinates, followed by conformational searching, and then a scan of
coordinates to estimate the cross-section.
Certainly with OB-2.2, you can generate 3D coordinates (e.g., obgen)
and run conformational searching (e.g., obconformer). You would then
need to write the code to extract cross-section from the 3D coordinates.
Cheers,
-Geoff
On Jan 20, 2009, at 4:46 AM, Strempel Sebastian wrote:
> Dear Geoffrey,
>
> is there any possibility to approximate the molecular cross-
> sectional diameter from a 2D SMILES with OpenBabel?
> If not could you point me in the right direction to search? Thank you.
>
> Best regards
>
> Sebastian

Patches item #2483731, was opened at 2009-01-03 15:11
Message generated for change (Comment added) made by egonw
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Category: None
Group: Accepted
>Status: Closed
>Resolution: Fixed
Priority: 5
Private: No
Submitted By: Egon Willighagen (egonw)
Assigned to: Egon Willighagen (egonw)
Summary: factoring out of ioformats
Initial Comment:
The CDK IO format definitions and matchers are quite useful outside the scope of just the CDK library, for example, for the core of Bioclipse. The IChemFormatMatcher implementations indeed do not depend on 'interfaces' or 'core' modules.
Only complication is that TestMethod and TestClass are being used, as well as DataFeatures. I have moved these into a second new module 'annotation' as they deal with meta data.
The branch egonw-ioformats is derived from cdk1.2.x/ and contains the necessary updates:
* three new modules: annotation, ioformats, test-ioformats
* new .cdkdepends etc for these
* @cdk.module updates
* replaces a use of MathTools.isOdd() with a local copy (one liner)
This patch is ready for review by two senior reviewers, as I like to see it included in the CDK 1.2.0 release.
Attached is a PNG with the new module dependency graph.
----------------------------------------------------------------------
>Comment By: Egon Willighagen (egonw)
Date: 2009-01-20 14:15
Message:
Applied to cdk1.2.x.
----------------------------------------------------------------------
Comment By: Egon Willighagen (egonw)
Date: 2009-01-19 11:56
Message:
Rajarshi, Stefan, thanx for reviewing!
----------------------------------------------------------------------
Comment By: Stefan Kuhn (shk3)
Date: 2009-01-19 11:47
Message:
Looks good for me
----------------------------------------------------------------------
Comment By: Egon Willighagen (egonw)
Date: 2009-01-05 10:44
Message:
Fixed the HIN one liner.
----------------------------------------------------------------------
Comment By: Egon Willighagen (egonw)
Date: 2009-01-04 18:35
Message:
Ack, on the HIN thingy. Will change that, and mention in the comment what
the math is supposed to test.
I agree on the three class (TestClass|-Method + DataFeatures) annotation
module... I could not think of a nicer solution. Fact is, that the
ioformats classes do use the annotation too. Putting them in interfaces
seemed weirder. Maybe it will grow in the future, if we start using more
annotation instead of JavaDoc... maybe for cdk.bug for not compiling
'buggy' code or so...
Anyway, if anyone knows a prettier solution for those three annotation
classes, please let me know.
----------------------------------------------------------------------
Comment By: Rajarshi Guha (rajarshi)
Date: 2009-01-04 16:48
Message:
In HINFormat.java, I would inline the test for odd numbers into the if
statement rather than making it a separate function. Also, it is a little
grating that a module will consist of 2 files - but if ti simplifies
dependencies that's good. Overall, it looks good to me and I sign off
----------------------------------------------------------------------
Comment By: Egon Willighagen (egonw)
Date: 2009-01-04 14:21
Message:
The full changelog:
commit 271122ed99c855d798810196ae86736df85223bc
Author: egonw <egonw@...>
Date: Sun Jan 4 09:39:24 2009 +0000
Added missing dependencies on the new ioformats module
git-svn-id:
https://cdk.svn.sourceforge.net/svnroot/cdk/cdk/branches/egonw-ioformats@...
eb4e18e3-b210-0410-a6ab-dec725
commit 585d12d4201982622dded11de2676861612ede0d
Author: egonw <egonw@...>
Date: Sat Jan 3 14:08:21 2009 +0000
Introduced a ioformats module (along with test-ioformats), which can
now be used without pulling interfaces, core and the
git-svn-id:
https://cdk.svn.sourceforge.net/svnroot/cdk/cdk/branches/egonw-ioformats@...
eb4e18e3-b210-0410-a6ab-dec725
commit de702bb7c1422c070feb459353b46df45a617bec
Author: egonw <egonw@...>
Date: Sat Jan 3 14:03:08 2009 +0000
Moved to the annotation module, allowing use of it without pulling
deps on interfaces and core too
git-svn-id:
https://cdk.svn.sourceforge.net/svnroot/cdk/cdk/branches/egonw-ioformats@...
eb4e18e3-b210-0410-a6ab-dec725
commit 02fefb7118b4a166de1a2fc8dabcc0b8ad8617c3
Author: egonw <egonw@...>
Date: Sat Jan 3 14:02:37 2009 +0000
Removed depedency on MathTools
git-svn-id:
https://cdk.svn.sourceforge.net/svnroot/cdk/cdk/branches/egonw-ioformats@...
eb4e18e3-b210-0410-a6ab-dec725
commit c7277db65b8ea6888c9f61335d698fc18f12afbb
Author: egonw <egonw@...>
Date: Sat Jan 3 14:02:10 2009 +0000
Moved the two annotation classes into a separate module
git-svn-id:
https://cdk.svn.sourceforge.net/svnroot/cdk/cdk/branches/egonw-ioformats@...
eb4e18e3-b210-0410-a6ab-dec725
commit 8a17b3a3313afe638fac99f397c4e513ee28fc6d
Author: egonw <egonw@...>
Date: Sat Jan 3 09:08:09 2009 +0000
Setting up a branch, to split up 'io' into 'io' and 'ioformats'.
git-svn-id:
https://cdk.svn.sourceforge.net/svnroot/cdk/cdk/branches/egonw-ioformats@...
eb4e18e3-b210-0410-a6ab-dec725
As done with Git. From the git-svn-id you can look up the SVN commit
revision. For example, the revision of the last patch is 13727, while
commit 13723 created the egonw-ioformats branch.
To review an individual patch, use this link:
http://cdk.svn.sourceforge.net/viewvc/cdk?view=rev&revision=13727
----------------------------------------------------------------------
Comment By: Egon Willighagen (egonw)
Date: 2009-01-04 14:18
Message:
A Nightly is running here:
http://pele.farmbio.uu.se/nightly-ioformats/
----------------------------------------------------------------------
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